docs(specs): fix README.md spec-number index drift and resolve collisions

[bug-ops]

Summary

• specs/README.md's Feature Docs table had drifted from the actual specs/ directory numbers across ~38 entries (the 017–056 range, off by one to two) — a contributor following the documented index would land on the wrong spec or a 404.
• Three spec numbers were double-assigned on disk: 016 (agent-feedback / output-filtering), 057 (agent-persistence / autoskill-versioned-merging), 058 (plugins / autoskill-query-rewriting). Renumbered the newer/less-cross-referenced directory in each pair — 016-agent-feedback → 054-agent-feedback (fills a pre-existing gap), 057-agent-persistence → 078-agent-persistence, 058-plugins → 079-plugins — and updated every cross-reference (specs/, AGENTS.md files, CHANGELOG.md path mentions, spec wikilinks). The AutoSkill A1–A6 (056–061) and Gonka/SpeculationEngine numbering runs were kept intact since they're internally cross-referenced by number in code and other specs.
• Corrected ~30 rustdoc citations across zeph-config, zeph-context, zeph-memory, zeph-agent-context, zeph-common, zeph-core, and src/init/mod.rs that mistakenly cited spec 064 (the permanent durable-execution slot) when they meant the MemGuard type-aware-retrieval spec at 004-memory/004-16-memory-type-aware-retrieval.md — a naming collision that spec's own info-callout already flagged as a known issue "for a future doc-only follow-up." Left the legitimate durable-execution spec 064/spec-064 citations in the same files untouched.
• Fixed a stray 018-index → 017-index reference in specs/MOC-specs.md.
• Added two previously-missing Feature Docs table rows for the renamed 078-agent-persistence and 079-plugins specs.
• Updated the "Housekeeping Note" in specs/064-durable-execution/spec.md to reflect that the collisions it flagged as out-of-scope are now resolved.

Docs-only change — no runtime logic modified, only doc/rustdoc comment text and directory names.

Closes #6308

Test plan

• cargo +nightly fmt --check
• cargo clippy --profile ci --workspace --all-targets --features "desktop,ide,server,chat,pdf,scheduler,testing" -- -D warnings
• cargo nextest run --config-file .github/nextest.toml --workspace --features "desktop,ide,server,chat,pdf,scheduler" --lib --bins (13792 passed; one unrelated timing-based concurrency test flaked once under load, confirmed passing in isolation and on a clean re-run of the full suite)
• RUSTFLAGS="-D warnings" RUSTDOCFLAGS="--deny rustdoc::broken_intra_doc_links" cargo doc --no-deps --workspace --features desktop,ide,server,chat,pdf,scheduler
• gitleaks protect --staged --no-banner --redact
• Verified zero duplicate spec numbers remain on disk and every path referenced in specs/README.md resolves to an existing file